I used this command:
vmd cfx.prmtop -cor md2.mdcrd
And it says,
ERROR>Error reading optional structure information from coordinate file
md2.mdcrd
ERROR>Will ignore structure information in this file.
Info>Using plugin cor for coordinates from file md2.mdcrd
ERROR>Incorrect number of atoms <0> in coordinate file md2.mdcrd
ERROR>Mismatch between existing molecule or structure file atom count and
coordinate or trajectory file atom count.
Info>Finished with coordinate file md2.mdcrd.
Best,
Wenze Gu
Department of Chemistry
Brown University
On Thu, Mar 1, 2018 at 7:02 PM, Carlos Simmerling <
carlos.simmerling.gmail.com> wrote:
> Sorry for the autocorrect. When you loaded the mdcrd file into that
> molecule what did it say?
>
> On Mar 1, 2018 7:02 PM, "Carlos Simmerling" <carlos.simmerling.gmail.com>
> wrote:
>
> > Then when you loaded the necessary file next, what exactly did VMD say?
> >
> > On Mar 1, 2018 6:44 PM, "Gu, Wenze" <wenze_gu.brown.edu> wrote:
> >
> >> Hi Carlos,
> >>
> >> Yes, I first loaded the prmtop file and then loaded the mdcrd file.
> After
> >> loaded the prmtop file, vmd said there are 38800 atoms.
> >>
> >> Best,
> >> Wenze Gu
> >> Department of Chemistry
> >> Brown University
> >>
> >> On Thu, Mar 1, 2018 at 2:37 PM, Carlos Simmerling <
> >> carlos.simmerling.gmail.com> wrote:
> >>
> >> > this was just discussed a few days ago on the list, most likely you
> are
> >> not
> >> > using the right format for the file in VMD.
> >> > Amber coordinates format is the trajectory file (mdcrd), restart
> format
> >> is
> >> > the restart file. did you load your prmtop first, then the mdcrd file
> as
> >> > coordinates format (or coordinates with box)?
> >> >
> >> > On Thu, Mar 1, 2018 at 2:16 PM, Gu, Wenze <wenze_gu.brown.edu> wrote:
> >> >
> >> > > Dear list,
> >> > >
> >> > > I ran amber MD with this .in file:
> >> > >
> >> > > md, npt, equilibrium to 300K quickly,
> >> > > &cntrl
> >> > > imin = 0, ntx = 7, irest = 1, ig=-1
> >> > > ntpr = 1000, ntwx = 1000, ntwe = 0, ntwprt=0, ntwr=50000,
> >> > > ntc = 2, ntf = 2, iwrap = 1, ioutfm = 1,
> >> > > nstlim = 10000000, dt =0.002,
> >> > > temp1=300.0, temp0 = 300.0, ntt =1, tautp =2.0,
> >> > > ntb = 2, ntp = 1, taup = 2.0, pres0 =1.0, cut = 12.0,
> >> > > &end
> >> > > END
> >> > > END
> >> > >
> >> > > However, when I tried to read the trajectory file in VMD, it says
> >> > incorrect
> >> > > number of atoms <0> in mdcrd file. Meanwhile, the prmtop file has
> >> normal
> >> > > number of atoms. Do you know what's going wrong here? Thanks!
> >> > >
> >> > > Best,
> >> > > Wenze Gu
> >> > > Department of Chemistry
> >> > > Brown University
> >> > > _______________________________________________
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> >> > >
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> >> >
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Received on Thu Mar 01 2018 - 16:30:03 PST
